RFLP for 16S rRNA - (May/02/2006 )

Hi there to all

Im working on Antarctic Bacteria. My project is to derieve a phylogenetic tree from microbial diversity of soil and sediment samples,. im facing some problems in my rflp that i have to do before sending in for sequencing. Currently im using [i]Hinf1, Ncl 1 and also Rsa 1. But this enzymes dont seem to give me good cuts. Can any suggest any other RE's for 16S rRNA gene.

Thank you loads,

Leela

-leela_t-

Basically you can use any RE. I would suggest using just grabbing a few REs at random from the freezer and try them - 10 should be enough to find a couple that work well.

-Daniel Tillett-

Hi,

if you have a sequence (evenif from related species) you can use several programs for finding appropriate enzymes, which produce sufficent numbers of fragments with suffcient size. Software: Vector NTi (now for free from invirogen), Bioedit etc. Its fatster & cheaper than to try for it in the lab.

hobglobin

-hobglobin-

QUOTE (Daniel Tillett @ May 2 2006, 04:44 AM)

Basically you can use any RE. I would suggest using just grabbing a few REs at random from the freezer and try them - 10 should be enough to find a couple that work well.

Hi there,

thanks for your suggestion. Actuallly im trrying out Hae III n Hind II. Im kind of using 6 RE for time being. Send in 8 sequences n to my pleasent suprise all were different bacteria's. Im so happy. Thanks again.

leela

-leela_t-